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lib/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm  view on Meta::CPAN

  Arg [1]    : ditag type
  Example    : @all_tags = @{$ditag_adaptor->fetch_by_dbID(1003)};
  Description: Retrieve ditags with a certain id from the database
  Returntype : Bio::EnsEMBL::Map::Ditag
  Caller     : general

=cut

sub fetch_by_dbID {
  my ($self, $tagid) = @_;

  if(!$tagid){
    throw "must be called with the type of a ditag.";
  }
  my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
                            FROM   ditag d
                            WHERE  d.ditag_id = ?");
  $sth->execute($tagid);
  my $result = $self->_fetch($sth);

  return $result->[0];
}


=head2 fetch_all_by_type

  Arg [1]    : ditag type
  Example    : @all_tags = @{$ditag_adaptor->fetch_by_type("SME005")};

lib/Bio/EnsEMBL/Utils/VegaCuration/Transcript.pm  view on Meta::CPAN

  my $self = shift;
  my ($gene,$gene_c,$trans_c) = @_;
  my $action = ($self->param('dry_run')) ? 'Would add' : 'Added';
  my $aa  = $gene->adaptor->db->get_AttributeAdaptor;
  my $dbh = $gene->adaptor->db->dbc->db_handle;

  #get list of IDs that have previously been sent to annotators
  my $seen_genes = $self->get_havana_fragmented_loci_comments;

  my $gsi    = $gene->stable_id;
  my $gid    = $gene->dbID;
  my $g_name;
  my $study_more = 1;
  eval {
    $g_name = $gene->display_xref->display_id;
  };	
  if ($@) {
    $g_name = $gene->get_all_Attributes('name')->[0]->value;
  }

  #get existing gene remarks